18-57588259-C-T

Position:

• chr18-57588259-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.156 in 152,240 control chromosomes in the GnomAD database, including 2,142 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.16 (2142 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.345

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.62).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.198 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.156 AC: 23756 AN: 152122 Hom.: 2142 Cov.: 33

Gnomad AFR AF: 0.0791

Gnomad AMI AF: 0.0735

Gnomad AMR AF: 0.172

Gnomad ASJ AF: 0.194

Gnomad EAS AF: 0.0117

Gnomad SAS AF: 0.154

Gnomad FIN AF: 0.219

Gnomad MID AF: 0.139

Gnomad NFE AF: 0.200

Gnomad OTH AF: 0.151

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.156 AC: 23760 AN: 152240 Hom.: 2142 Cov.: 33 AF XY: 0.157 AC XY: 11663 AN XY: 74422

Gnomad4 AFR AF: 0.0789

Gnomad4 AMR AF: 0.172

Gnomad4 ASJ AF: 0.194

Gnomad4 EAS AF: 0.0118

Gnomad4 SAS AF: 0.155

Gnomad4 FIN AF: 0.219

Gnomad4 NFE AF: 0.200

Gnomad4 OTH AF: 0.148

Alfa AF: 0.163 Hom.: 276

Bravo AF: 0.147

Asia WGS AF: 0.0860 AC: 300 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.62
CADD	Benign	1.0
DANN	Benign	0.91

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs34779648; hg19: chr18-55255491;